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(-) Description

Title :  CRYSTAL STRUCTURE OF A DINB HOMOLOG (DBH) LESION BYPASS DNA POLYMERASE CATALYTIC FRAGMENT FROM SULFOLOBUS SOLFATARICUS
 
Authors :  J. D. Pata, B. L. Zhou, T. A. Steitz
Date :  09 May 01  (Deposition) - 12 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Polymerase Palm, Thumb, Fingers, Helix-Hairpin-Helix, Fidelity, Processivity, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Zhou, J. D. Pata, T. A. Steitz
Crystal Structure Of A Dinb Lesion Bypass Dna Polymerase Catalytic Fragment Reveals A Classic Polymerase Catalytic Domain.
Mol. Cell V. 8 427 2001
PubMed-ID: 11545744  |  Reference-DOI: 10.1016/S1097-2765(01)00310-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DBH
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNHIS-DBH-216
    Expression System Strain: HMS174(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL CATALYTIC DOMAIN (RESIDUES 2-216)
    Gene: DBH
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: DBH BYPASS POLYMERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , TYR A:10 , TYR A:48 , ARG A:51 , LYS A:160 , HOH A:2010 , HOH A:2035 , HOH A:2068 , HOH A:2069 , HOH A:2086BINDING SITE FOR RESIDUE SO4 A 2001
2AC2SOFTWAREHIS A:0 , ASN A:20 , GLN A:22 , LYS A:26 , ARG A:77BINDING SITE FOR RESIDUE SO4 A 2002
3AC3SOFTWAREGLY A:188 , SER A:189 , HOH A:2031 , HOH A:2074BINDING SITE FOR RESIDUE SO4 A 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IM4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IM4)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.DPO4_SULSF3-188  1A:3-188

(-) Exons   (0, 0)

(no "Exon" information available for 1IM4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:205
 aligned with DPO4_SULSF | P96022 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:209
                                1                                                                                                                                                                                                            
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196         
           DPO4_SULSF     - ----MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRD 205
               SCOP domains d1im4a_ A: DinB homolog (DBH)                                                                                                                                                                                     SCOP domains
               CATH domains 1im4A01       -------------------------------------------------------------------1im4A01 A:-3-10,A:78-178  [code=3.30.70.270, no name defined]                                        --------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.hhhhhhhhhhhhhhh...eeeeee.----..eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh...eeeeee..eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh....eee.hhhhhhhhhhh..hhhh...hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------UMUC  PDB: A:3-188 UniProt: 3-188                                                                                                                                                         ----------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1im4 A  -3 HHHHHIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYS----TSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRD 205
                                     6        16        26       | -  |     46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196         
                                                                34   39
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IM4)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPO4_SULSF | P96022)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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UniProtKB/Swiss-Prot
        DPO4_SULSF | P96022: 1k1q 1k1s

(-) Related Entries Specified in the PDB File

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